Research workbench
Crystal structure of E. COLI seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine
Analyse Crystal structure of E. COLI seryl-tRNA synthetase complexed to seryl sulfamoyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R1M
- Type
- protein
- Length
- 855 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--tRNA ligase
- EC
- 6.1.1.11
- UniProt
- A0A1X3JK72
- Ligands
- SSA, PO4
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--tRNA ligase (EC 6.1.1.11) | protein | 427 | 46% helix, 21% strand | A0A1X3JK72 |
| B | Serine--tRNA ligase (EC 6.1.1.11) | protein | 428 | 45% helix, 21% strand | A0A1X3JK72 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.83 | 0.98 | 31 | EDO |
| 2 | 603 | 0.75 | 0.82 | 56 | SSA |
| 3 | 590 | 0.72 | 0.80 | 46 | SSA, PO4 |
| 4 | 70 | 0.41 | 0.80 | 13 | empty |
| 5 | 72 | 0.40 | 0.80 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 2700 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 6R1M · Crystal structure of E. coli seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A1X3JK72
- Elsewhere: RCSB PDB 6R1M · PDBe 6R1M · UniProt A0A1X3JK72
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